Proteomics platform tools
List of proteomics tools
- msconvert: tool to convert raw and standard ms format to standard ms format (open source tool from Proteowizard).
- peakaboo: peak picking tool for high resolution MS data (open source tool from Proteowizard).
Analytical Biochemistry (RUG, PIs: Peter Horvatovich and Rainer Bischoff)
- TAPP pipeline (Frank Suits, IBM Watson Center) for quantitative processing of single stage LC-MS data. Able to process data obtained with mass spectrometer of different resolution
- grid: read mzdata.xml or mzxml data, mesh the raw to given resolution (other type of function are available too)
- centroid: feature quantification tool, read the output of grid and provide the list of detected feature
- Warp2D: time alignment of features list provided by the centroid module ref
- metamatch: matching the same features across multiple feature list (chromatograms) resulting in a quantitative matrix of the matched features in different chromatograms
- msCompare (Berend Hoekman) is a framework interconnecting feature quantification and feature matching modules of different single stage quantitative data processing workflow. The included data rpocessing wrokflwos are the following:
- MZmine feature quantification and feature matching module
- OpenMS feature quantification and feature matching module
- SuperHirn feature quantification and feature matching module
- M-N rules feature quantification
- inhouse matching module including Warp2D
- Time alignment algorithms using high quality preselected mass traces developed by Christin Christin (only Matlab script is currently available)
Bioinformatics Laboratory (AMC, PIs: Antoine van Kampen, Perry Moerland, and Silvia Olabarriaga)
- Statistical data analysis pipeline for pre-processed quantitative MS data
- readAPML: R script for converting an aligned APML file to (an external representation of) an ExpressionSet class for further analysis with R/Bioconductor.
- QC: R script for quality control.
- DE: R script for differential expression analysis.
- CL: R script for classification.
Steps for adding tools to Netherlands Bioinformatics for Proteomics Platform (NBPP)
- rename the template excel sheet (tool_workflow_template_final.xls) to your tool name. The excel sheet you can download from the root directory of the FTP server.
- fill the excel sheet
- login to the FTP server and make a directory with the tool name
- upload the filled excel sheet, the tool, the example input and output files
- add your tool to the list of Platform tool with explanation to NBIC Wiki: https://wiki.nbic.nl/index.php/Platform_tool
The FTP server is setup in a way that you can create a directory and place any files on it, but you can't delete them. If you need to delete files, then send email to Ishtiaq Ahmad (RUG) and/or Peter Horvatovich (RUG).